libs/phylogeny/tests/readTreeWithComments.cpp | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 add missing includes required by gcc-5

libs/phylogeny/tests/Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 current dir is not in path by default

programs/Makefile.generic | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 fix install target by creating install dir if needed

libs/phylogeny/likeDist.cpp | 4 2 + 2 - 0 !
libs/phylogeny/likeDistfixRoot.cpp | 4 2 + 2 - 0 !
libs/phylogeny/numRec.cpp | 2 1 + 1 - 0 !
programs/fastml/bb_options_list.h | 4 2 + 2 - 0 !
programs/fastml/mainbb.cpp | 6 3 + 3 - 0 !
programs/gainLoss/computeCorrelations.cpp | 2 1 + 1 - 0 !
programs/gainLoss/gainLoss.cpp | 2 1 + 1 - 0 !
7 files changed, 12 insertions(+), 12 deletions(-)

 fix some spelling issues

programs/Makefile.generic | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 avoid that tests fail simply because of a missing test directory

libs/phylogeny/tests/Makefile | 121 115 + 6 - 0 !
1 file changed, 115 insertions(+), 6 deletions(-)

 document what tests are failing and how they failed

libs/phylogeny/Makefile | 6 3 + 3 - 0 !
libs/phylogeny/tests/Makefile | 4 2 + 2 - 0 !
programs/Makefile.generic | 6 3 + 3 - 0 !
3 files changed, 8 insertions(+), 8 deletions(-)

 remove all instances of -ftemplate-depth
 With C++-11 the template depth is 1024, and g++ defaults to 900, 
 hence there is no need to set a lower value that makes the
 compilation fail. 

libs/phylogeny/errorMsg.cpp | 4 2 + 2 - 0 !
libs/phylogeny/someUtil.cpp | 8 4 + 4 - 0 !
programs/fastml/bbReport.cpp | 2 1 + 1 - 0 !
3 files changed, 7 insertions(+), 7 deletions(-)

 replace comparisons of std::*stream 
 It is no longer possible to compare std::*stream to NULL or
 to each other, hence use .good() in the first case and compare
 the pointers in the second one.